Merge pull request #3 from FCP-INDI/0.3.4_development

0.3.4 development
Changed the version number from 0.3.3 to 0.3.4.
Widened the 'Create FSL Model' button so that the whole button label
would be visible.
Implemented the basic checkbox grid GUI interface for the group analysis
model builder. More work is needed to fully integrate it further.
Creation of the checkbox_grid wxPython widget for the renovated group
analysis model builder.
Removed a space.
Introduced a check which ensures all input file paths provided in the pipeline configuration yaml file exist before actually running the pipeline.
Updated version information (for development stage).
Added BET as an option for skull-stripping, and introduced Krishna's MeanFD fix.
Repackaged install script.
Add BET option to config write.
Added constants for the 3dAutoMask & BET forking option.
Introduced a working version of the new ANTS interfaces (specifically for antsRegistration and antsApplyWarps, removing deprecated antsIntroduction.sh and WarpImageMultiTransform), introduced a range of GUI bug fixes and improvements, merged in some of the additions from the 0.3.4a hotfix, introduced major re-organization, documentation and clean-up of cpac_pipeline.py.
Added file containing the "change_transform_type" function for updating func->anat bbreg affines post-conversion to ITK format.
Merge branch 'master' of https://github.com/sgiavasis/C-PAC

Conflicts:
	CPAC/pipeline/cpac_pipeline.py
Merge branch 'new_gpa_model_builder'

Conflicts:
	CPAC/__init__.py
	CPAC/pipeline/cpac_pipeline.py
Resolved three GUI-based errors which previously obfuscated user experience (two involving pipeline creation errors and one involving pipeline name conflicts), and wrote new documentation for some of the legacy GUI code.
Removed potential errors where the user could change the filename of a pipeline config .yml file but leave the pipelineName attribute the same, then try to load - this would create conflicts if another config .yml was loaded with the same pipelineName but different filepath. Improved some cpac_pipeline.py code as well.
Update README.md
Introduced the option to run repeated measures in group-level analysis, and included changes to the subject list generator so that it automatically creates a group analysis subject list and a phenotype file template pre-formatted for running repeated measures.